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All Facilities >> Dana-Farber Cancer Institute >> DFCI-Molecular Biology Core Facilities (Genomics / Genome Analysis and Technologies)

DFCI-Molecular Biology Core Facilities (Genomics / Genome Analysis and Technologies)

Facility Details

About This Facility

Services and Equipment

Publications

Associations

Metadata

Dana-Farber Cancer Institute

Dana-Farber Cancer Institute

mail:450 Brookline Ave physical address: 21 Burlington Ave

Boston, MA 02215

United States

http://mbcf.dfci.harvard.edu

Quicklinks:

https://coremarketplace.org/dfcimbcf https://coremarketplace.org/RRID:SCR_018264

Facility LIMS Page

http://mbcf.dfci.harvard.edu

Primary Contact:

Paul Morrison

Last Updated: 04/01/2020

Facility RRID

RRID:SCR_018264

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Facility Details

The Molecular Biology Core Facilities (MBCF) at Dana-Farber Cancer Institute (DFCI) offers a full suite of services for a wide variety of genomic next-generation sequencing (NGS) library preparation, sequencing and analysis applications including RNAseq, ChIPseq, ATACseq, CRISPR screening, whole genome methylation profiling, targeted resequencing, single-cell RNAseq, exome sequencing, and more. The genomics core technology platforms include Illumina NovaSeq6000, NextSeq500s, MiSeqs, MiniSeq.

High throughput sample preparation is performed on Beckman Coulter Biomek FX and i7 systems. Low throughput precious samples are prepared by experienced technical staff.

The MBCF writes and maintains standardized pipelines for routine NGS analysis such as RNAseq, ChIPseq, and CRISPR screening. Complex bioinformatics analysis such as integration of multi-omics datasets or specialized analyses can be performed by the experienced computational biology team.

Genomics email: zachary_herbert@dfci.harvard.edu
Proteomics email: james_lee@dfci.harvard.edu
and everything: paul_morrison@dfci.harvard.edu

Facility Policies

Services are offerred outside of Dana-Farber Cancer Institute

Consulting is offerred outside of Dana-Farber Cancer Institute

(To see more facility information, click the in the upper right)

Services offered:

Amino Acid Analysis

Computational - Bioinformatics

Copy Number Variation (CNV)

Data Processing And Interpretation

Mass Spectrometry

Phosphoproteomics

Sample Preparation

Sequencing - DNA Sequencing

Sequencing - Next Generation Sequencing (NGS)

Surface Plasmon Resonance (SPR)

Facility Equipment

Some Equipment:
Illumina NovaSe 6000
Illumina MiSeq DNA Sequencer (3)
Illumina NextSeq 500 (5)

Multitude of QC instrumentation to ensure samples going into genomic sequencing will produce high quality data

(To see more facility information, click the in the upper right)

Publications

Publications associated with this facility (Click To View):

1.) Herbert ZT, Thimmapuram J, Xie S, Kershner JP, Kolling FW, Ringelberg CS, LeClerc A, Alekseyev YO, Fan J, Podnar JW, Stevenson HS, Sommerville G, Gupta S, Berkeley M, Koeman J, Perera A, Scott AR, Grenier JK, Malik J, Ashton JM, Pivarski KL, Wang X, Kuffel G, Mesa TE, Smith AT, Shen J, Takata Y, Volkert TL, Love JA, Zhang Y, Wang J, Xuei X, Adams M, Levine SS (2020 Jan 10). Multisite Evaluation of Next-Generation Methods for Small RNA Quantification. PMID: 31966025.

2.) da Silva A, Bowden M, Zhang S, Masugi Y, Thorner AR, Herbert ZT, Zhou CW, Brais L, Chan JA, Hodi FS, Rodig S, Ogino S, Kulke MH (2018 Oct). Characterization of the Neuroendocrine Tumor Immune Microenvironment. PMID: 30153220.

3.) Herbert ZT, Kershner JP, Butty VL, Thimmapuram J, Choudhari S, Alekseyev YO, Fan J, Podnar JW, Wilcox E, Gipson J, Gillaspy A, Jepsen K, BonDurant SS, Morris K, Berkeley M, LeClerc A, Simpson SD, Sommerville G, Grimmett L, Adams M, Levine SS (2018 Mar 15). Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction. PMID: 29703133.

4.) Pomerantz MM, Spisák S, Jia L, Cronin AM, Csabai I, Ledet E, Sartor AO, Rainville I, O (2017 Sep 15). The association between germline BRCA2 variants and sensitivity to platinum-based chemotherapy among men with metastatic prostate cancer. PMID: 28608931.

5.) Townsend EC, Murakami MA, Christodoulou A, Christie AL, Köster J, DeSouza TA, Morgan EA, Kallgren SP, Liu H, Wu SC, Plana O, Montero J, Stevenson KE, Rao P, Vadhi R, Andreeff M, Armand P, Ballen KK, Barzaghi-Rinaudo P, Cahill S, Clark RA, Cooke VG, Davids MS, DeAngelo DJ, Dorfman DM, Eaton H, Ebert BL, Etchin J, Firestone B, Fisher DC, Freedman AS, Galinsky IA, Gao H, Garcia JS, Garnache-Ottou F, Graubert TA, Gutierrez A, Halilovic E, Harris MH, Herbert ZT, Horwitz SM, Inghirami G, Intlekofer AM (2016 Jul 11). The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice. PMID: 27479034.

6.) Townsend EC, Murakami MA, Christodoulou A, Christie AL, Köster J, DeSouza TA, Morgan EA, Kallgren SP, Liu H, Wu SC, Plana O, Montero J, Stevenson KE, Rao P, Vadhi R, Andreeff M, Armand P, Ballen KK, Barzaghi-Rinaudo P, Cahill S, Clark RA, Cooke VG, Davids MS, DeAngelo DJ, Dorfman DM, Eaton H, Ebert BL, Etchin J, Firestone B, Fisher DC, Freedman AS, Galinsky IA, Gao H, Garcia JS, Garnache-Ottou F, Graubert TA, Gutierrez A, Halilovic E, Harris MH, Herbert ZT, Horwitz SM, Inghirami G, Intlekofer AM (2016 Apr 11). The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice. PMID: 27070704.

7.) Spisák S, Lawrenson K, Fu Y, Csabai I, Cottman RT, Seo JH, Haiman C, Han Y, Lenci R, Li Q, Tisza V, Szállási Z, Herbert ZT, Chabot M, Pomerantz M, Solymosi N, GAME-ON/ELLIPSE Consortium., Gayther SA, Joung JK, Freedman ML (2015 Nov). CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants. PMID: 26398868.

8.) Solomon KR, Sharma P, Chan M, Morrison PT, Finberg RW (2004 Mar 3). CD109 represents a novel branch of the alpha2-macroglobulin/complement gene family. PMID: 14980714.

9.) Maulik G, Shrikhande A, Kijima T, Ma PC, Morrison PT, Salgia R (2002 Feb). Role of the hepatocyte growth factor receptor, c-Met, in oncogenesis and potential for therapeutic inhibition. PMID: 11750879.

10.) Sattler M, Pisick E, Morrison PT, Salgia R (2000). Role of the cytoskeletal protein paxillin in oncogenesis. PMID: 10795627.

11.) Kolodner RD, Hall NR, Lipford J, Kane MF, Morrison PT, Finan PJ, Burn J, Chapman P, Earabino C, Merchant E (1995 Jan 15). Structure of the human MLH1 locus and analysis of a large hereditary nonpolyposis colorectal carcinoma kindred for mlh1 mutations. PMID: 7812952.

12.) Bronner CE, Baker SM, Morrison PT, Warren G, Smith LG, Lescoe MK, Kane M, Earabino C, Lipford J, Lindblom A (1994 Mar 17). Mutation in the DNA mismatch repair gene homologue hMLH1 is associated with hereditary non-polyposis colon cancer. PMID: 8145827.

13.) Morrison PT, Lovett ST, Gilson LE, Kolodner R (1989 Jul). Molecular analysis of the Escherichia coli recO gene. PMID: 2544549.

14.) Kolodner R, Evans DH, Morrison PT (1987 Aug). Purification and characterization of an activity from Saccharomyces cerevisiae that catalyzes homologous pairing and strand exchange. PMID: 3303029.

15.) Symington LS, Morrison PT, Kolodner R (1984). Genetic recombination catalyzed by cell-free extracts of Saccharomyces cerevisiae. PMID: 6397323.

16.) Doherty MJ, Morrison PT, Kolodner R (1983 Jul 5). Genetic recombination of bacterial plasmid DNA. Physical and genetic analysis of the products of plasmid recombination in Escherichia coli. PMID: 6308264.

17.) James AA, Morrison PT, Kolodner R (1982 Sep 25). Genetic recombination of bacterial plasmid DNA. Analysis of the effect of recombination-deficient mutations on plasmid recombination. PMID: 6759658.

18.) James AA, Morrison PT, Kolodner R (1983 May 19-25). Isolation of genetic elements that increase frequencies of plasmid recombinants. PMID: 6341860.

(To see more facility information, click the in the upper right)

Associations

NERLSCD

Northeast Regional Life Science Core Directors

Cancer Center

ABRF

Association of Biomolecular Resource Facilities

(To see more facility information, click the in the upper right)

Metadata

Links

All the links listed resolve to this core listing

https://coremarketplace.org/?FacilityID=57
https://coremarketplace.org/dfcimbcf
https://coremarketplace.org/RRID:SCR_018264

SciCrunch Data Imports (data maintained by https://scicrunch.org)

Keywords:

Next generation sequencing, RNAseq, ChIPseq, ATACseq, CRISPR, analysis, dataset, genomics, core facility, USEDit

Resource Type:

Resource, service resource, core facility, access service resource

Citation:

Dana-Farber Cancer Institute Molecular Biology Core Facility (RRID:SCR_018264)

(To see more facility information, click the in the upper right)

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DFCI-Molecular Biology Core Facilities (Genomics / Genome Analysis and Technologies)

Facility Details

About This Facility

Services and Equipment

Publications

Associations

Metadata

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